Combined Transcriptomics and Proteomics Forecast Analysis for Potential Genes Regulating the Columbian Plumage Color in Chickens

Abstract Background Coloration is one of the most recognizable characteristics in chickens, and clarifying the coloration mechanisms will help us understand feather color formation. “Yufen I” is an commercial egg-laying chicken breed in China, that was developed by a three-line cross using lines H, N and D. Columbian plumage is a typical feather character of the “Yufen I” H line. In order to understand the molecular mechanism underlying pigmentation of Columbian plumage, this study utilizes high-throughput sequencing technology to compare differences in transcriptomics and proteomics in different feather follicular tissue, including the dorsal neck with black and white striped feather follicles (Group A) and the ventral neck with white feather follicles (Group B) in the “Yufen I” H line. Results In this study, we identified a total of 21,306 genes and 5203 proteins in chicken feather follicles. Among these, 209 genes and 382 proteins were differentially expressed in two different locations, Group A and Group B, respectively. A total of 8 differentially expressed genes (DEGs) and 9 differentially expressed proteins (DEPs) were found to be involved in the melanogenesis pathway. Besides, a specifically expressed MED23 gene and a differential expressed GNAQ protein were involved in melanin synthesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis mapped 190 DEGs and 322 DEPs, to 175 and 242 pathways, respectively, and there were 166 pathways correlated with both DEGs and DEPs. 49 DEPs/DEGs overlapped and were enriched for 12 pathways. Transcriptomic and proteomic analyses revealed that the following pathways were activated: melanogenesis, cardiomycete adrenergic, calcium and the cGMP-PKG. The expression of DEGs was validated by real-time quantitative polymerase chain reaction (qRT-PCR) that was similar to that of RNA-seq. In addition, we found that MED23, FZD10, WNT7B and WNT11 genes expression peaked at approximately 8 weeks in the “Yufen I” H line, which is consistent with the molting cycle. As both the groups showed significant differences in terms of expression of the genes studied, this study opens up avenues for study in the future to assess their exact function in color of plumage. Conclusion These common DEGs and DEPs were enriched in the melanogenesis pathway. The MED23 and GNAQ were also reported to have a crucial part synthesis of melanin. In addition, this study is the first to reveal variations in gene and protein in the “Yufen I” H line during Columbian feather color development, and discover principal genes and proteins that would aid in the functional genomics studies in future. The results of the present study provide a significant conceptual basis for the “Yufen I” H line future breeding schemes and provide a basis for research on the mechanisms of feather pigmentation.